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- PDB-6ofd: The crystal structure of octadecyloxy(naphthalen-1-yl)methylphosp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ofd | |||||||||
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Title | The crystal structure of octadecyloxy(naphthalen-1-yl)methylphosphonic acid in complex with red kidney bean purple acid phosphatase | |||||||||
![]() | Fe(3+)-Zn(2+) purple acid phosphatase | |||||||||
![]() | METAL BINDING PROTEIN / Purple acid phosphatase / metallohydrolases / transition state / catalysis / osteoporosis | |||||||||
Function / homology | ![]() acid phosphatase / acid phosphatase activity / ferric iron binding / zinc ion binding / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Feder, D. / Schenk, G. / Guddat, L.W. / Hussein, W.M. / McGeary, R.P. / Kan, M.W. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Synthesis, evaluation and structural investigations of potent purple acid phosphatase inhibitors as drug leads for osteoporosis. Authors: Feder, D. / Kan, M.W. / Hussein, W.M. / Guddat, L.W. / Schenk, G. / McGeary, R.P. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 420.3 KB | Display | ![]() |
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PDB format | ![]() | 338.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6of5C ![]() 4dhlS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 4 molecules ABDC
#1: Protein | Mass: 52926.434 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Sugars , 6 types, 17 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #4: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #5: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #6: Polysaccharide | alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #9: Sugar | ChemComp-NAG / |
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-Non-polymers , 10 types, 1744 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/MF1.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/MF1.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#7: Chemical | ChemComp-ZN / #8: Chemical | ChemComp-FE / #10: Chemical | ChemComp-MF1 / [( | #11: Chemical | ChemComp-NA / #12: Chemical | ChemComp-SO4 / #13: Chemical | ChemComp-EDO / #14: Chemical | #15: Chemical | ChemComp-GOL / | #16: Chemical | ChemComp-CL / | #17: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.45 Å3/Da / Density % sol: 64.32 % / Description: Hexagonal |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion / pH: 4 Details: 2.3 M ammonium sulfate, 0.1 M sodium acetate, pH 4.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 28, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20.05 Å / Num. obs: 139709 / % possible obs: 99.8 % / Redundancy: 5.2 % / CC1/2: 0.997 / Rpim(I) all: 0.048 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.2→2.225 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 4624 / CC1/2: 0.763 / Rpim(I) all: 0.293 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4DHL Resolution: 2.2→20.045 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0.28 / Phase error: 18.04
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→20.045 Å
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Refine LS restraints |
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LS refinement shell |
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